Hello Freesurfer support team,
I am trying to create accurate white/pial surfaces, however, due to signal drop-out, Freesurfer is consistently underestimating the pial surface -- a problem which I am only able to fix using control points. Unfortunately, while adding cps does push the pial surface outward, it creates inaccurate/biased white surfaces which would skew thickness estimates (etc.).
As such, I would like to use the white surface generated using the command recon-all -autorecon2 -subjid <subjid> -mprage -hires (created before cp incorporation) and the pial surface generated using the command recon-all -autorecon2-cp -subjid <subjid> -mprage -hires (created after cp incorporation) to run the last step of recon-all autorecon3.
Which files should I copy over?
So far I have tried copying the files noted below from the pre-cp directory into the post-cp directory and tried running autorecon3 with no success.
Thanks in advance.
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TRIAL #1:
Copied these files from pre-cp directory to post-cp directory:
?h.white.preaparc
?h.white.preaparc.H
?h.white.preaparc.K
Got this error message:
#@# Jacobian white lh Thu Jul 18 17:49:33 EDT 2019
/home/smithe16/freesurfer/subjects/April_29_2019_0100_combined/scripts
mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
reading surface from ../surf/lh.white.preaparc...
mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match ../surf/lh.white.preaparc
No such file or directory
mrisReadTriangleFile failed.
No such file or directory
mris_jacobian: could not read target surface ../surf/lh.sphere.reg
No such file or directory
Linux cynthia 4.4.0-145-generic #171-Ubuntu SMP Tue Mar 26 12:43:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s April_29_2019_0100_combined exited with ERRORS at Thu Jul 18 17:49:35 EDT 2019
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TRIAL #2:
Copied these files from pre-cp directory to post-cp directory:
?h.white.preaparc
?h.white.preaparc.H
?h.white.preaparc.K
?h.inflated
?h.inflated.H
?h.inflated.K
?h.smoothwm
?h.sphere
Got this error message:
1 Reading lh.sulc
MRISreadNewCurvature: incompatible vertex number in file ../surf/lh.sulc
No such file or directory
MRISregister: could not read curvature file 'lh.sulc'
No such file or directory
Linux cynthia 4.4.0-145-generic #171-Ubuntu SMP Tue Mar 26 12:43:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s April_29_2019_0100_combined_2 exited with ERRORS at Fri Jul 19 12:43:09 EDT 2019